Turkeys were allowed to roam free in agricultural fields, eating whatever they found, especially insect pests that threatened the crops

Turkeys were instead kept in pens or otherwise confined in domestic contexts and fed table scraps or other leftover/surplus portions of human food.

The assumptions behind the tests were that if Theory 1 is correct, the turkeys would have isotope ratios significantly different from those of humans, reflecting a diet based on local plants and insects or other small animals, whereas if Theory 2 is correct, the turkeys would have isotope ratios similar to those of humans, since they would be eating the same types of food, mostly maize. The main sample of turkey bones tested came from Shields Pueblo near Cortez, Colorado, which was occupied primarily during the Pueblo II and Pueblo III periods (ca. 1020 to 1280 AD) and has been extensively excavated by Crow Canyon Archaeological Center. This site is particularly well suited to this kind of study because it has one of the largest and best documented samples of faunal remains known in the area. Bone samples from jackrabbits and cottontails found at Shields were also tested to provide a control sample of animals that would certainly have been mainly eating local plants rather than maize. The ratios were compared to those from earlier tests on human remains from the region, as well as a set of turkey bones from a wide variety of other sites in southwestern Colorado dating over a long period of time, including the outlying Chacoan great house known as Escalante Pueblo.

Blocked-In Kiva at Escalante Pueblo

The results were quite straightforward, and they clearly supported Theory 2. The isotope ratios were very similar to those from human samples, showing extensive reliance on maize and little to no meat consumption, and quite different from the rabbit samples, which showed more reliance on native plants. This was the case not only for the Shields Pueblo samples but also for those from other sites, and there was no clear evidence of change over time. All of the turkey remains gave results in the same narrow range, regardless of site or time period. The obvious conclusion is that turkeys were being kept in pens or other confined spaces in domestic contexts, and were fed table scraps or surplus cornmeal. The authors also suggest another possible conclusion:

There is another behavioral explanation (besides feeding of surplus maize/table scraps) for the similarity in stable carbon and nitrogen isotopes between turkeys and humans. It is possible that turkeys were fed human fecal waste. The practice of feeding waste to livestock is not unheard of in prehistory.

. . .

While there are no records of turkey being fed human waste, it is common for turkeys to eat their own waste as well as the waste of other fowl. Given that maize does not completely digest in the human gut, it is certainly possible that some food was obtained in this way.

The only evidence they cite for this interpretation, however, comes from Korean pig raising, and as they note there is no evidence at all that anything similar was ever done with turkeys, in the Southwest or elsewhere. Given that lack of evidence, I find this idea implausible. Table scraps from human meals and/or surplus or specially prepared cornmeal seem like much more reasonable ways turkeys would have been fed.Rawlings, T., & Driver, J. (2010). Paleodiet of domestic turkey, Shields Pueblo (5MT3807), Colorado: isotopic analysis and its implications for care of a household domesticate Journal of Archaeological Science, 37 (10), 2433-2441 DOI: 10.1016/j.jas.2010.05.004